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Calcium in PDB 4qnp: Crystal Structure of the 2009 Pandemic H1N1 Influenza Virus Neuraminidase with A Neutralizing Antibody

Enzymatic activity of Crystal Structure of the 2009 Pandemic H1N1 Influenza Virus Neuraminidase with A Neutralizing Antibody

All present enzymatic activity of Crystal Structure of the 2009 Pandemic H1N1 Influenza Virus Neuraminidase with A Neutralizing Antibody:
3.2.1.18;

Protein crystallography data

The structure of Crystal Structure of the 2009 Pandemic H1N1 Influenza Virus Neuraminidase with A Neutralizing Antibody, PDB code: 4qnp was solved by H.Q.Wan, H.Yang, D.A.Shore, R.J.Garten, L.Couzens, J.Gao, L.L.Jiang, P.J.Carney, J.Villanueva, J.Stevens, M.C.Eichelberger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.85 / 2.80
Space group C 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 144.290, 202.951, 143.968, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the 2009 Pandemic H1N1 Influenza Virus Neuraminidase with A Neutralizing Antibody (pdb code 4qnp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the 2009 Pandemic H1N1 Influenza Virus Neuraminidase with A Neutralizing Antibody, PDB code: 4qnp:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4qnp

Go back to Calcium Binding Sites List in 4qnp
Calcium binding site 1 out of 4 in the Crystal Structure of the 2009 Pandemic H1N1 Influenza Virus Neuraminidase with A Neutralizing Antibody


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the 2009 Pandemic H1N1 Influenza Virus Neuraminidase with A Neutralizing Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:75.4
occ:1.00
 O A:GLY298 2.3 42.4 1.0
O A:ASP294 2.4 46.1 1.0
O A:GLY342 2.6 65.7 1.0
O A:ASN344 2.6 60.6 1.0
OD2 A:ASP324 2.7 43.3 1.0
O A:HOH635 2.7 59.6 1.0
C A:GLY298 3.3 43.5 1.0
C A:GLY342 3.5 63.0 1.0
CG A:ASP324 3.6 44.3 1.0
C A:ASP294 3.6 43.2 1.0
C A:ASN344 3.8 56.9 1.0
O A:HOH601 3.8 32.9 1.0
CA A:GLY342 4.0 62.8 1.0
N A:SER299 4.1 42.6 1.0
CA A:SER299 4.1 42.9 1.0
N A:GLY298 4.1 46.0 1.0
CB A:ASP324 4.2 47.3 1.0
CA A:GLY298 4.2 44.9 1.0
O A:ALA343 4.3 50.4 1.0
C A:ALA343 4.3 53.4 1.0
OD1 A:ASP324 4.4 39.5 1.0
CA A:GLY345 4.4 46.9 1.0
N A:ALA343 4.4 57.5 1.0
N A:ASN295 4.5 41.2 1.0
CA A:ASN295 4.5 42.6 1.0
CA A:ASP294 4.5 43.7 1.0
N A:GLY345 4.6 51.4 1.0
N A:ASN344 4.6 54.4 1.0
CB A:ASP294 4.6 45.5 1.0
O A:ASN341 4.6 72.3 1.0
N A:ASP294 4.7 40.1 1.0
CA A:ALA343 4.8 54.4 1.0
CA A:ASN344 4.8 56.9 1.0
O A:PRO326 4.8 55.5 1.0
C A:ASN295 5.0 46.6 1.0
CB A:SER299 5.0 42.2 1.0

Calcium binding site 2 out of 4 in 4qnp

Go back to Calcium Binding Sites List in 4qnp
Calcium binding site 2 out of 4 in the Crystal Structure of the 2009 Pandemic H1N1 Influenza Virus Neuraminidase with A Neutralizing Antibody


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the 2009 Pandemic H1N1 Influenza Virus Neuraminidase with A Neutralizing Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:91.0
occ:1.00
 OD1 A:ASP384 2.3 72.8 1.0
OD1 A:ASP376 2.5 50.5 1.0
OD2 A:ASP376 2.7 48.2 1.0
O A:ASN386 2.7 57.8 1.0
CG A:ASP376 2.9 44.9 1.0
OD1 A:ASN378 3.0 78.4 1.0
CG A:ASP384 3.3 58.0 1.0
O A:ASP384 3.4 59.2 1.0
C A:ASN386 3.8 63.8 1.0
C A:ASP384 3.8 58.9 1.0
CG A:ASN378 3.9 64.2 1.0
OD2 A:ASP384 3.9 57.6 1.0
N A:ASN386 4.0 68.1 1.0
ND2 A:ASN378 4.2 70.5 1.0
CA A:ASN386 4.3 68.9 1.0
CB A:ASP376 4.3 41.6 1.0
CA A:GLY379 4.4 43.9 1.0
C A:ASN385 4.4 66.5 1.0
CB A:ASP384 4.4 58.2 1.0
CA A:ASP384 4.4 54.8 1.0
N A:GLY379 4.5 45.0 1.0
N A:ASN385 4.5 63.5 1.0
N A:ASP384 4.5 50.7 1.0
C A:ASN378 4.6 46.6 1.0
OG A:SER319 4.7 43.8 1.0
CB A:ASN386 4.8 76.4 1.0
CA A:ASN385 4.8 63.9 1.0
O A:ASN378 4.8 47.0 1.0
N A:PHE387 4.9 59.3 1.0
N A:ASN378 4.9 42.9 1.0

Calcium binding site 3 out of 4 in 4qnp

Go back to Calcium Binding Sites List in 4qnp
Calcium binding site 3 out of 4 in the Crystal Structure of the 2009 Pandemic H1N1 Influenza Virus Neuraminidase with A Neutralizing Antibody


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the 2009 Pandemic H1N1 Influenza Virus Neuraminidase with A Neutralizing Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca505

b:72.2
occ:1.00
 O B:ASP294 2.2 45.4 1.0
O B:ASN344 2.3 63.2 1.0
O B:GLY342 2.4 68.9 1.0
O B:GLY298 2.7 54.2 1.0
OD2 B:ASP324 2.9 46.4 1.0
O B:HOH611 2.9 51.8 1.0
C B:GLY342 3.4 68.8 1.0
C B:ASP294 3.4 45.1 1.0
C B:ASN344 3.5 58.7 1.0
C B:GLY298 3.6 50.3 1.0
CG B:ASP324 3.7 48.7 1.0
C B:ALA343 4.0 61.9 1.0
O B:ALA343 4.1 61.6 1.0
CA B:GLY342 4.1 67.4 1.0
CA B:ASN295 4.2 42.6 1.0
N B:ASN344 4.2 59.6 1.0
CA B:GLY345 4.2 45.9 1.0
N B:ASN295 4.2 43.5 1.0
N B:GLY298 4.2 51.2 1.0
N B:ALA343 4.3 68.9 1.0
N B:GLY345 4.3 50.7 1.0
N B:SER299 4.4 48.0 1.0
OD1 B:ASP324 4.4 45.6 1.0
CB B:ASP324 4.4 50.4 1.0
CA B:SER299 4.5 44.6 1.0
CA B:GLY298 4.5 49.4 1.0
CA B:ASN344 4.5 60.7 1.0
CA B:ASP294 4.5 45.5 1.0
CA B:ALA343 4.5 66.0 1.0
C B:ASN295 4.6 44.2 1.0
CB B:ASP294 4.7 48.5 1.0
O B:ASN341 4.7 58.7 1.0
N B:ASP294 4.7 44.5 1.0
OD1 B:ASP294 5.0 51.9 1.0

Calcium binding site 4 out of 4 in 4qnp

Go back to Calcium Binding Sites List in 4qnp
Calcium binding site 4 out of 4 in the Crystal Structure of the 2009 Pandemic H1N1 Influenza Virus Neuraminidase with A Neutralizing Antibody


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the 2009 Pandemic H1N1 Influenza Virus Neuraminidase with A Neutralizing Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca506

b:88.7
occ:1.00
 OD1 B:ASP376 2.5 47.8 1.0
OD2 B:ASP376 2.5 48.6 1.0
OD1 B:ASP384 2.6 78.5 1.0
CG B:ASP376 2.8 44.2 1.0
O B:ASN386 2.8 68.3 1.0
OD1 B:ASN378 3.1 77.6 1.0
O B:ASP384 3.4 59.2 1.0
CG B:ASP384 3.4 62.8 1.0
ND2 B:ASN386 3.5 99.1 1.0
C B:ASP384 3.8 59.3 1.0
OD2 B:ASP384 3.9 65.3 1.0
CG B:ASN378 3.9 65.1 1.0
C B:ASN386 3.9 66.9 1.0
N B:ASN386 4.1 67.9 1.0
ND2 B:ASN378 4.2 73.9 1.0
CA B:GLY379 4.2 40.0 1.0
CB B:ASP376 4.3 41.5 1.0
CB B:ASP384 4.4 58.8 1.0
CA B:ASP384 4.4 55.5 1.0
N B:GLY379 4.4 42.4 1.0
N B:ASP384 4.5 50.7 1.0
CG B:ASN386 4.5 97.5 1.0
C B:ASN385 4.5 67.2 1.0
C B:ASN378 4.5 45.0 1.0
N B:ASN385 4.5 64.8 1.0
CA B:ASN386 4.5 73.6 1.0
OG B:SER319 4.7 42.4 1.0
O B:ASN378 4.7 43.5 1.0
CA B:ASN385 4.8 66.2 1.0
N B:ASN378 4.9 43.5 1.0
O B:GLY382 5.0 40.8 1.0
CB B:SER319 5.0 40.9 1.0

Reference:

H.Q.Wan, H.Yang, D.A.Shore, R.J.Garten, L.Couzens, J.Gao, L.L.Jiang, P.J.Carney, J.Villanueva, J.Stevens, M.C.Eichelberger. Structural Characterization of A Protective Epitope Spanning A(H1N1)PDM09 Influenza Virus Neuraminidase Monomers Nat Commun 2015.
ISSN: ESSN 2041-1723
DOI: 10.1038/NCOMMS7114
Page generated: Sun Jul 14 12:30:28 2024

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